Chromosome-level genome assembly of Murraya paniculata sheds light on biosynthesis of floral volatiles.

Murraya / chemistry Phylogeny Flowers / genetics Chromosomes
Citrus species Comparative genomics Flower volatiles Murraya paniculata Phenylacetaldehyde Transposon

Journal

BMC biology
ISSN: 1741-7007
Titre abrégé: BMC Biol
Pays: England
ID NLM: 101190720

Informations de publication

Date de publication:
20 06 2023
Historique:
received: 08 11 2022
accepted: 31 05 2023
medline: 22 6 2023
pubmed: 21 6 2023
entrez: 20 6 2023
Statut: epublish

Résumé

Murraya paniculata (L.) Jack, commonly called orange jessamine in the family Rutaceae, is an important ornamental plant in tropical and subtropical regions which is famous for its strong fragrance. Although genome assemblies have been reported for many Rutaceae species, mainly in the genus Citrus, full genomic information has not been reported for M. paniculata, which is a prerequisite for in-depth genetic studies on Murraya and manipulation using genetic engineering techniques. Here, we report a high-quality chromosome-level genome assembly of M. paniculata and aim to provide insights on the molecular mechanisms of flower volatile biosynthesis. The genome assembly with a contig N50 of 18.25 Mb consists of 9 pseudomolecules and has a total length of 216.86 Mb. Phylogenetic analysis revealed that M. paniculata diverged from the common ancestor approximately 25 million years ago and has not undergone any species-specific whole genome duplication events. Genome structural annotation and comparative genomics analysis revealed that there are obvious differences in transposon contents among the genomes of M. paniculata and Citrus species, especially in the upstream regions of genes. Research on the flower volatiles of M. paniculata and C. maxima at three flowering stages revealed significant differences in volatile composition with the flowers of C. maxima lacking benzaldehyde and phenylacetaldehyde. Notably, there are transposons inserted in the upstream region of the phenylacetaldehyde synthase (PAAS) genes Cg1g029630 and Cg1g029640 in C. maxima, but not in the upstream region of three PAAS genes Me2G_2379, Me2G_2381, and Me2G_2382 in M. paniculata. Our results indicated that compared to the low expression levels of PAAS genes in C. maxima, the higher expression levels of the three PAAS genes in M. paniculata are the main factor affecting the phenylacetaldehyde biosynthesis and causing the content difference of phenylacetaldehyde. The phenylacetaldehyde synthetic activities of the enzymes encoded by M. paniculata PAAS genes were validated by in vitro analyses. Our study provides useful genomic resources of M. paniculata for further research on Rutaceae plants, identifies new PAAS genes, and provides insights into how transposons contribute to variations in flower volatiles among Murraya and Citrus plants.

Sections du résumé

BACKGROUND
Murraya paniculata (L.) Jack, commonly called orange jessamine in the family Rutaceae, is an important ornamental plant in tropical and subtropical regions which is famous for its strong fragrance. Although genome assemblies have been reported for many Rutaceae species, mainly in the genus Citrus, full genomic information has not been reported for M. paniculata, which is a prerequisite for in-depth genetic studies on Murraya and manipulation using genetic engineering techniques. Here, we report a high-quality chromosome-level genome assembly of M. paniculata and aim to provide insights on the molecular mechanisms of flower volatile biosynthesis.
RESULTS
The genome assembly with a contig N50 of 18.25 Mb consists of 9 pseudomolecules and has a total length of 216.86 Mb. Phylogenetic analysis revealed that M. paniculata diverged from the common ancestor approximately 25 million years ago and has not undergone any species-specific whole genome duplication events. Genome structural annotation and comparative genomics analysis revealed that there are obvious differences in transposon contents among the genomes of M. paniculata and Citrus species, especially in the upstream regions of genes. Research on the flower volatiles of M. paniculata and C. maxima at three flowering stages revealed significant differences in volatile composition with the flowers of C. maxima lacking benzaldehyde and phenylacetaldehyde. Notably, there are transposons inserted in the upstream region of the phenylacetaldehyde synthase (PAAS) genes Cg1g029630 and Cg1g029640 in C. maxima, but not in the upstream region of three PAAS genes Me2G_2379, Me2G_2381, and Me2G_2382 in M. paniculata. Our results indicated that compared to the low expression levels of PAAS genes in C. maxima, the higher expression levels of the three PAAS genes in M. paniculata are the main factor affecting the phenylacetaldehyde biosynthesis and causing the content difference of phenylacetaldehyde. The phenylacetaldehyde synthetic activities of the enzymes encoded by M. paniculata PAAS genes were validated by in vitro analyses.
CONCLUSIONS
Our study provides useful genomic resources of M. paniculata for further research on Rutaceae plants, identifies new PAAS genes, and provides insights into how transposons contribute to variations in flower volatiles among Murraya and Citrus plants.

Identifiants

DOI: 10.1186/s12915-023-01639-6 PMID: 37340448 PMC: PMC10283294
pubmed: 37340448
doi: 10.1186/s12915-023-01639-6
pii: 10.1186/s12915-023-01639-6
pmc: PMC10283294
doi:

Substances chimiques

phenylacetaldehyde U8J5PLW9MR

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

142

Informations de copyright

© 2023. The Author(s).

Références

Mol Plant. 2020 Aug 3;13(8):1194-1202
pubmed: 32585190
Nucleic Acids Res. 2005 Nov 28;33(20):6494-506
pubmed: 16314312
Nucleic Acids Res. 2019 May 7;47(8):e47
pubmed: 30783653
Nature. 2018 Feb 15;554(7692):311-316
pubmed: 29414943
J Biol Chem. 2006 Aug 18;281(33):23357-66
pubmed: 16766535
Bioinformatics. 2021 Apr 1;36(22-23):5516-5518
pubmed: 33325502
Nucleic Acids Res. 2019 Jul 2;47(W1):W5-W10
pubmed: 31062021
Nucleic Acids Res. 2019 Jan 8;47(D1):D807-D811
pubmed: 30395283
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Plant J. 2020 Dec;104(5):1215-1232
pubmed: 32985030
Mol Biol Evol. 2015 Apr;32(4):835-45
pubmed: 25739733
Nat Genet. 2017 May;49(5):765-772
pubmed: 28394353
Mol Plant. 2019 Jul 1;12(7):935-950
pubmed: 30999079
Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5589-94
pubmed: 15064405
Funct Plant Biol. 2015 Sep;42(9):851-857
pubmed: 32480727
Nucleic Acids Res. 2022 Jan 7;50(D1):D27-D38
pubmed: 34718731
Phytochemistry. 2009 Jul-Aug;70(11-12):1428-34
pubmed: 19747702
Bioinformatics. 2008 Mar 1;24(5):637-44
pubmed: 18218656
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
Mol Biol Evol. 2021 Dec 9;38(12):5825-5829
pubmed: 34597405
Phytopathology. 2019 Dec;109(12):2064-2073
pubmed: 31425000
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
Plant Physiol. 2017 Apr;173(4):2225-2242
pubmed: 28196843
Nat Biotechnol. 2014 Jul;32(7):656-62
pubmed: 24908277
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
pubmed: 15961478
Nat Biotechnol. 2019 Aug;37(8):907-915
pubmed: 31375807
Ecol Lett. 2010 May;13(5):643-56
pubmed: 20337694
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Mol Biol Evol. 2007 Aug;24(8):1586-91
pubmed: 17483113
Mol Plant. 2022 Dec 5;15(12):1841-1851
pubmed: 36307977
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Hortic Res. 2022 Feb 19;:
pubmed: 35184178
Nat Commun. 2019 Apr 2;10(1):1494
pubmed: 30940818
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296
pubmed: 33885785
Plant J. 2007 Mar;49(5):840-54
pubmed: 17316174
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Bioinformatics. 2020 Apr 1;36(7):2253-2255
pubmed: 31778144
Phytopathology. 2018 Sep;108(9):1089-1094
pubmed: 29648945
Cell Syst. 2016 Jul;3(1):99-101
pubmed: 27467250
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108
pubmed: 33575650
Curr Protoc Bioinformatics. 2014 Dec 12;48:4.11.1-4.11.39
pubmed: 25501943
J Chem Ecol. 2018 Apr;44(4):397-405
pubmed: 29500752
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Mol Plant. 2022 Oct 3;15(10):1503-1505
pubmed: 36004795
Mol Ecol Resour. 2021 Oct;21(7):2533-2545
pubmed: 34145765
PLoS Genet. 2013;9(2):e1003255
pubmed: 23408902
NAR Genom Bioinform. 2020 Jun;2(2):lqaa026
pubmed: 32440658
Gene. 2017 Aug 30;626:14-25
pubmed: 28476688
Bioinformatics. 2020 May 1;36(9):2896-2898
pubmed: 31971576
Nat Genet. 2013 Jan;45(1):59-66
pubmed: 23179022
Plant Cell. 2012 Mar;24(3):1242-55
pubmed: 22427337
Genome Biol. 2019 Dec 16;20(1):275
pubmed: 31843001
Plant Physiol. 2000 Mar;122(3):627-33
pubmed: 10712525
Nucleic Acids Res. 2012 Jan;40(Database issue):D1178-86
pubmed: 22110026
BMC Bioinformatics. 2021 Nov 25;22(1):566
pubmed: 34823473
Genome Biol. 2008 Jan 11;9(1):R7
pubmed: 18190707
J Pharm Biomed Anal. 2011 Dec 15;56(5):950-61
pubmed: 21885228
Mol Plant. 2018 Aug 6;11(8):1024-1037
pubmed: 29885473
Plant Biol (Stuttg). 2019 Sep;21(5):899-910
pubmed: 30866144
Nat Rev Genet. 2007 Dec;8(12):973-82
pubmed: 17984973
Science. 2008 Apr 25;320(5875):486-8
pubmed: 18436778
Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190347
pubmed: 32075564

Auteurs

Tianyu Yang (T)

School of Life Science, Yunnan University, Kunming, 650500, China.
Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China.
Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.

Xin Yin (X)

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China.
Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
ORCID: 0000-0003-2664-2637

Haotong Kang (H)

Key Laboratory of Plant Resources Conservation and Utilization, College of Biological Resources and Environmental Sciences, Jishou University, Jishou, 416000, China.

Danni Yang (D)

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China.
Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.

Xingyu Yang (X)

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China.
Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.

Yunqiang Yang (Y)

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China. yangyunqiang@mail.kib.ac.cn.
Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. yangyunqiang@mail.kib.ac.cn.
Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. yangyunqiang@mail.kib.ac.cn.

Yongping Yang (Y)

Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, China. yangyp@mail.kib.ac.cn.
Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. yangyp@mail.kib.ac.cn.
Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. yangyp@mail.kib.ac.cn.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Rutaceae › Murraya › Chromosome-level genome assembly of Murraya...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Chromosome-level genome assembly of Murraya...
questionsmedicales.fr › Structures de plante › Parties aériennes de plante › Sommités fleuries › Fleurs › Chromosome-level genome assembly of Murraya...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Chromosomes › Chromosome-level genome assembly of Murraya...